In a large skillet, heat olive oil over medium heat. Add onions and sauté 2-3 minutes until softened and slightly translucent.
Add the red bell pepper and continue cooking another 2-3 minutes. Add the zucchini, squash and kosher salt. Stir to combine and place a tight fitting lid on the pan. Cook 5-7 minutes, stirring occasionally until vegetables have softened slightly.
Add the can of tomatoes, the garlic, red pepper flakes, thyme, rosemary and dried basil and stir to blend. Cook an additional 8-10 minutes with the lid on the pan, stirring occasionally.